Commits for cricket

v266_preview to v266_preview2 (2012-04-10 to 2012-04-17) v266

• DEPRECATING OLD FORMATS1) Changed the order of formatChecker to group like with like 2) Changed wig and bedGraph validation to say submit as a bigWig 3) Changed fasta to say submit as a fastQ 4) Dropped peptideMapping and rpkm as one was a freepass and the other was an ill defined special case format for Caltech 5) Dropped PSL as we don't accept it, but kept code so that we could have it on file. 6) Changed tagAlign and pairedTagAligh to say submit as BAM 7) I also kept the bedGraph validator as example code in the comments, not sure if we need it 8) I left bedFloat and csqual and csfasta as I do not have clear directive.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 202, context: html, text, full: html, text
• Ever improving usage statement
  • src/hg/encode/validateFiles/validateFilesUsage - lines changed 30, context: html, text, full: html, text
• Moving the as files to the lib/encode directory so they are all together at least.
  • src/hg/encode/autoSql/README - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/autoSql/bedLogR.as - lines changed 14, context: html, text, full: html, text
  • src/hg/encode/autoSql/bedLogR.sql - lines changed 22, context: html, text, full: html, text
  • src/hg/encode/autoSql/bedRnaElements.as - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/autoSql/bedRnaElements.sql - lines changed 20, context: html, text, full: html, text
  • src/hg/encode/autoSql/bedRrbs.as - lines changed 15, context: html, text, full: html, text
  • src/hg/encode/autoSql/bedRrbs.sql - lines changed 23, context: html, text, full: html, text
  • src/hg/lib/encode/bedLogR.as - lines changed 14, context: html, text, full: html, text
  • src/hg/lib/encode/bedLogR.sql - lines changed 22, context: html, text, full: html, text
  • src/hg/lib/encode/bedRnaElements.as - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/encode/bedRnaElements.sql - lines changed 20, context: html, text, full: html, text
  • src/hg/lib/encode/bedRrbs.as - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/encode/bedRrbs.sql - lines changed 23, context: html, text, full: html, text
• Makeing the chromStart and chromEnd standard uint and standardizing the descriptions
  • src/hg/lib/encode/wgEncodeGencodeExonSupport.as - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/encode/wgEncodeGencodePolyAFeature.as - lines changed 7, context: html, text, full: html, text
• First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
  • src/hg/lib/encode/cshlShortTransfrag.as - lines changed 30, context: html, text, full: html, text
• First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
  • src/hg/lib/encode/bedLogR.as - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/encode/bedRnaElements.as - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/encode/bedRrbs.as - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/encode/broadPeak.as - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/encode/chiaPet.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/gappedPeak.as - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/encode/narrowPeak.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/encode/tagAlign.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/wgEncodeGencodeExonSupport.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/wgEncodeGencodePolyAFeature.as - lines changed 2, context: html, text, full: html, text
• Chia pet was never used, we used bed12 instead. shortFrags are download only
  • src/hg/lib/encode/chiaPet.as - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/encode/chiaPet.sql - lines changed 19, context: html, text, full: html, text
  • src/hg/lib/encode/obsolete/shortFrags.as - lines changed 31, context: html, text, full: html, text
  • src/hg/lib/encode/obsolete/shortFrags.sql - lines changed 37, context: html, text, full: html, text
  • src/hg/lib/encode/shortFrags.as - lines changed 31, context: html, text, full: html, text
  • src/hg/lib/encode/shortFrags.sql - lines changed 37, context: html, text, full: html, text
• Start of a test suite
  • src/hg/encode/validateFiles/tests/goodMaleHg18.pairedTagAlign - lines changed 63, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg18.tagAlign - lines changed 150, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed3 - lines changed 90, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed4 - lines changed 92, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed5 - lines changed 91, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed6 - lines changed 91, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak - lines changed 94, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode/validateFiles/tests/goodMalehg19.bedRnaElements - lines changed 624500, context: html, text, full: html, text
• moved to downloads dir, these shouldnt be in the tree
  • src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCaltechRnaSeq.hg18.soft - lines changed 1712, context: html, text, full: html, text
  • src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlLongRnaSeq.hg18.soft - lines changed 111, context: html, text, full: html, text
  • src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.hg18.soft - lines changed 339, context: html, text, full: html, text
  • src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.hg19.soft - lines changed 407, context: html, text, full: html, text
  • src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwChIPSeq.hg18.soft - lines changed 4436, context: html, text, full: html, text
  • src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwDgf.hg19.soft - lines changed 448, context: html, text, full: html, text
• Adding more test files
  • src/hg/encode/validateFiles/tests/goodFemaleHg19.narrowPeak - lines changed 40, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodHg19.fastq - lines changed 100, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg18.bedGraph - lines changed 29, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed7 - lines changed 141884, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed8 - lines changed 141885, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed9 - lines changed 141886, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bedRrbs - lines changed 141887, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodNoGenderHg19.bedLogR - lines changed 69, context: html, text, full: html, text
• Adding and improving test cases
  • src/hg/encode/validateFiles/tests/goodFemaleHg18.gappedPeak - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodFemaleHg19.bed10 - lines changed 34, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodFemaleHg19.bed11 - lines changed 35, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodFemaleHg19.bed12 - lines changed 35, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodHg18.fasta - lines changed 50, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodHg19.csfasta - lines changed 49, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodHg19.csqual - lines changed 49, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed8 - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bed9 - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodMaleHg19.bedRrbs - lines changed 5, context: html, text, full: html, text
  • src/hg/encode/validateFiles/tests/goodNoGenderHg19.bed15 - lines changed 40, context: html, text, full: html, text
• Changing score to int to match bed standard
  • src/hg/lib/encode/gappedPeak.as - lines changed 1, context: html, text, full: html, text
• Fixing short labels to be shorter
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra - lines changed 22, context: html, text, full: html, text
• Removed an extra tab and the zero length line
  • src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak - lines changed 1, context: html, text, full: html, text
• Fixing steves requests #1664
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra - lines changed 22, context: html, text, full: html, text